Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1686
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 28570
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:334 original size:1 final size:1
Alignment explanation
Indices: 328--429 Score: 78
Period size: 1 Copynumber: 102.0 Consensus size: 1
318 ATTATGCCTG
* * * * * * * * *
328 AAAAAAAAAGAGACAAAAAACAAAAAAAAACAAAAAAACAAAAAAAACAACAAAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
393 AACAAAAAAAGAAAAAAGAAAAAAAGAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
430 TCAAGATGAA
Statistics
Matches: 73, Mismatches: 28, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 73 1.00
ACGTcount: A:0.86, C:0.08, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:354 original size:20 final size:17
Alignment explanation
Indices: 328--429 Score: 98
Period size: 18 Copynumber: 5.6 Consensus size: 17
318 ATTATGCCTG
* *
328 AAAAAAAAAGAGACAAA
1 AAAAAAAAAAAAACAAA
*
345 AAACAAAAAAAAACAAAA
1 AAAAAAAAAAAAAC-AAA
363 AAACAAAAAAAACAACAAA
1 AAA-AAAAAAAA-AACAAA
*
382 AAAAAACAAAAAACAAA
1 AAAAAAAAAAAAACAAA
399 AAAAGAAAAAAGAAA-AAA
1 AAAA-AAAAAA-AAACAAA
417 AGAAAAAGAAAAA
1 A-AAAAA-AAAAA
430 TCAAGATGAA
Statistics
Matches: 72, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
17 21 0.29
18 25 0.35
19 23 0.32
20 3 0.04
ACGTcount: A:0.86, C:0.08, G:0.06, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAACAAA
Found at i:365 original size:30 final size:30
Alignment explanation
Indices: 342--402 Score: 108
Period size: 29 Copynumber: 2.1 Consensus size: 30
332 AAAAAGAGAC
342 AAAA-AACAAAAAAAAACAAAAAAACAAAA
1 AAAACAACAAAAAAAAACAAAAAAACAAAA
371 AAAACAACAAAAAAAAAC-AAAAAACAAAA
1 AAAACAACAAAAAAAAACAAAAAAACAAAA
400 AAA
1 AAA
403 GAAAAAAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 18 0.58
30 13 0.42
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (30 bp):
AAAACAACAAAAAAAAACAAAAAAACAAAA
Found at i:381 original size:37 final size:38
Alignment explanation
Indices: 329--409 Score: 121
Period size: 37 Copynumber: 2.2 Consensus size: 38
319 TTATGCCTGA
*
329 AAAAAAAAGAGACAAAAAACAAA-AAAAAACAAAAAAAC
1 AAAAAAAACAGACAAAAAA-AAACAAAAAACAAAAAAAC
*
367 AAAAAAAACA-ACAAAAAAAAACAAAAAACAAAAAAAG
1 AAAAAAAACAGACAAAAAAAAACAAAAAACAAAAAAAC
404 AAAAAA
1 AAAAAA
410 GAAAAAAAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
36 3 0.08
37 28 0.70
38 9 0.22
ACGTcount: A:0.86, C:0.10, G:0.04, T:0.00
Consensus pattern (38 bp):
AAAAAAAACAGACAAAAAAAAACAAAAAACAAAAAAAC
Found at i:423 original size:37 final size:35
Alignment explanation
Indices: 331--429 Score: 110
Period size: 36 Copynumber: 2.7 Consensus size: 35
321 ATGCCTGAAA
* *
331 AAAAAAGAGACAAAAAACAAAAAAAAACAAAAAAAC
1 AAAAAAGA-AAAAAAAAAAAAAAAAAACAAAAAAAC
*
367 AAAAAA-AACAACAAAAAAAAACAAAAAACAAAAAAAG
1 AAAAAAGAA-AA-AAAAAAAAA-AAAAAACAAAAAAAC
* *
404 AAAAAAGAAAAAAAGAAAAAGAAAAA
1 AAAAAAGAAAAAAAAAAAAAAAAAAA
430 TCAAGATGAA
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
34 1 0.02
35 7 0.13
36 22 0.41
37 22 0.41
38 2 0.04
ACGTcount: A:0.86, C:0.08, G:0.06, T:0.00
Consensus pattern (35 bp):
AAAAAAGAAAAAAAAAAAAAAAAAAACAAAAAAAC
Found at i:1919 original size:75 final size:76
Alignment explanation
Indices: 1256--2573 Score: 1073
Period size: 74 Copynumber: 17.9 Consensus size: 76
1246 TCTTTCAAGA
*
1256 ATTTTTTTCAATTTCT-ATTTTTCAAAAAATCAACTCATATTGCAGA-GTGAGTTGAGCCTCGGG
1 ATTTTTTT-AATTTCTGTTTTTTCAAAAAATCAACTCATATTGCAGAGGTGAGTTGAGCCTCGGG
*
1319 TCACTC-GAGGT
65 TCACGCTGAGGT
* *
1330 A-TTTTTAAATTTC----TTTTCAAAAAATCAACTCATA-TGCAGAAGTGAGTTGAGCCTCGGGT
1 ATTTTTTTAATTTCTGTTTTTTCAAAAAATCAACTCATATTGCAGAGGTGAGTTGAGCCTCGGGT
1389 CACGCTGAGGT
66 CACGCTGAGGT
* *
1400 ATTTCTTTTAAATCTCTGTTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCG
1 ATTT-TTTT-AATTTCTGTTTTTTCAAAAAATCAACTCATATTGC-AGAGGTGAGTTGAGCCTCG
1465 GGTCAC-CTGAGGT
63 GGTCACGCTGAGGT
** *
1478 ATTTCAATTTATGTTTTCTG-TTTTTCAAAAAAATCAACT-ATATTGCGAGAAGTGAGTTGAGCC
1 ATTT---TTT-TAATTTCTGTTTTTTC-AAAAAATCAACTCATATTGC-AGAGGTGAGTTGAGCC
1541 TCGGGTCGCACGCTGAGGT
60 TCGGGT--CACGCTGAGGT
1560 A-TTTTTTAATTTC---TTTTTCAAAAAATCAACTCATATTGCAGAGGTGAGTTGAGCCTCGGGT
1 ATTTTTTTAATTTCTGTTTTTTCAAAAAATCAACTCATATTGCAGAGGTGAGTTGAGCCTCGGGT
1621 CACGCTGAGGT
66 CACGCTGAGGT
* * *
1632 ATTTTCATTT-TTTTTTCTTTTTTCAAAAAATCAACTCATA-TG-AGA-GTGAGTTGAGCCTC-G
1 ATTTT--TTTAATTTCTGTTTTTTCAAAAAATCAACTCATATTGCAGAGGTGAGTTGAGCCTCGG
1692 GTCACGCTGAGGT
64 GTCACGCTGAGGT
* *
1705 ATTTTCTTTAAATCTCTG-TTTTTCAAAAAAATAAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 ATTTT-TTT-AATTTCTGTTTTTTC-AAAAAATCAACTCATATTGC-AGAGGTGAGTTGAGCCTC
1769 GGGTCACGCTGAGGT
62 GGGTCACGCTGAGGT
* * *
1784 ATCTTTTT-ATTTCTCTGTTTTTCAAAAAAATCAACTCATAATGC-GAGAGTGAGTTG-GCCTC-
1 ATTTTTTTAATTTCTGT-TTTTTC-AAAAAATCAACTCATATTGCAGAG-GTGAGTTGAGCCTCG
1845 GGTCACGCTGAGGT
63 GGTCACGCTGAGGT
1859 ATTTTTTTAATTTCTGTTTTTTCAAAAAATCAACTCATATTGCAGAGGTGAGTTGAGCCTCGGGT
1 ATTTTTTTAATTTCTGTTTTTTCAAAAAATCAACTCATATTGCAGAGGTGAGTTGAGCCTCGGGT
*
1924 CATGCTGAGGT
66 CACGCTGAGGT
*
1935 A-TTTTTTATTTTCTG-TTTTTCAAAAAATCAACT--TATTGC-GAGAGTGAGTTG-GCCTCGGG
1 ATTTTTTTAATTTCTGTTTTTTCAAAAAATCAACTCATATTGCAGAG-GTGAGTTGAGCCTCGGG
1994 TCACGCTGA--T
65 TCACGCTGAGGT
* *
2004 ATTTCTTTTTAATTTCTGTTTTTT--AAAATTCAACTCA-AATGC-GAGAGTGAG-TGAGCCCTC
1 A-TT-TTTTTAATTTCTGTTTTTTCAAAAAATCAACTCATATTGCAGAG-GTGAGTTGAG-CCTC
2064 GGGTCACGCTGA-G-
62 GGGTCACGCTGAGGT
* * *
2077 ATATTTTTAA--TATGTCTTTTT---AAAATCAACT-ATA--ACAGAGG-GAGTTG-GCCTC-GG
1 ATTTTTTTAATTTCTGT-TTTTTCAAAAAATCAACTCATATTGCAGAGGTGAGTTGAGCCTCGGG
* *
2131 ACA-GTGTGAGGT
65 TCACG-CTGAGGT
* * * * **
2143 A--TTTTTAAGTTATGTTTTTT---TAAATCAACTC-TA-TACAGAGGTG-G-TGAG-CTTTGG-
1 ATTTTTTTAATTTCTGTTTTTTCAAAAAATCAACTCATATTGCAGAGGTGAGTTGAGCCTCGGGT
** *
2197 -ACGCATTCGAT
66 CACGC-TGAGGT
*
2208 ATTTCTTTTAATTTCTGTTTTTTC--AAAAT-AACTCATATTGCGAAAGGTGAAGTTGAGCCTCG
1 ATTT-TTTTAATTTCTGTTTTTTCAAAAAATCAACTCATATTGC-AGAGGTG-AGTTGAGCCTCG
* * *
2270 GGTCACAC-CA-TT
63 GGTCACGCTGAGGT
* * ** *
2282 ATTTCTTTTAAATTAT-TTTTTAAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCT--G
1 ATTT-TTTTAATTTCTGTTTTTTCAAAAAATCAACTCATATTGC-AGAGGTGAGTTGAGCCTCGG
** *
2344 GAAAAGC-GA-GT
64 GTCACGCTGAGGT
**
2355 ATTAATTTAAAATTTCTG-TTTTTC-AAAAATCCAACTCATATTGGCGAGAGGTGAGTTGAGGCC
1 ATT--TTTTTAATTTCTGTTTTTTCAAAAAAT-CAACTCATATT-GC-AGAGGTGAGTTGA-GCC
*
2418 TCGGGTCACGCCGAGGT
60 TCGGGTCACGCTGAGGT
* *
2435 A-TTCTTCAA-TTCATG-TTTTTCAAAAAATACAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
1 ATTTTTTTAATTTC-TGTTTTTTCAAAAAAT-CAACTCATATTGC-AGAGGTGAGTTGAGCCTCG
*
2497 GGGCACATG-TCGAGGT
63 GGTCAC--GCT-GAGGT
** * * * *
2513 A--TTTTCGATTT-TG-TTTTTC-GAAGATCAACTCATAAT-CAAGAGGTGAGTTGAGTCTCGGG
1 ATTTTTTTAATTTCTGTTTTTTCAAAAAATCAACTCATATTGC-AGAGGTGAGTTGAGCCTCGGG
2572 TC
65 TC
2574 GCGACAGCCG
Statistics
Matches: 1051, Mismatches: 95, Indels: 197
0.78 0.07 0.15
Matches are distributed among these distances:
63 1 0.00
64 15 0.01
65 30 0.03
66 21 0.02
67 6 0.01
68 31 0.03
69 65 0.06
70 13 0.01
71 47 0.04
72 65 0.06
73 103 0.10
74 164 0.16
75 109 0.10
76 80 0.08
77 95 0.09
78 90 0.09
79 79 0.08
80 23 0.02
81 6 0.01
82 8 0.01
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (76 bp):
ATTTTTTTAATTTCTGTTTTTTCAAAAAATCAACTCATATTGCAGAGGTGAGTTGAGCCTCGGGT
CACGCTGAGGT
Found at i:2474 original size:152 final size:149
Alignment explanation
Indices: 1268--2573 Score: 1091
Period size: 152 Copynumber: 8.9 Consensus size: 149
1258 TTTTTTCAAT
* *
1268 TTCTATTTTTCAAAAAATCAACTCATATTGC-AGA-GTGAGTTGAGCCTCGGGTCACTC-GAGGT
1 TTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTCACGCTGAGGT
*
1330 ATTTTTAAATTTC---TTTTCAAAAAATCAACTCATA-TGC-AGAAGTGAGTTGAGCCTCGGGTC
65 ATTTTTTAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAG-AGTGAGTTGAGCCTCGGGTC
1390 ACGCTGAGGTATTTCTTTTAAA
129 ACGCTGAGGTATTTCTTTT-AA
*
1412 TCTCTGTTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC-CTGAG
1 T-TCTG-TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTCACGCTGAG
*
1476 GTATTTCAATTTATGTTTTCTGTTTTTCAAAAAAATCAACT-ATATTGCGAGAAGTGAGTTGAGC
63 GTATTT---TTTA--ATTTCTGTTTTTC-AAAAAATCAACTCATATTGCGAG-AGTGAGTTGAGC
1540 CTCGGGTCGCACGCTGAGGTA-TT-TTTTAA
121 CTCGGGT--CACGCTGAGGTATTTCTTTTAA
*
1569 TT-TCTTTTTCAAAAAATCAACTCATATTGC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
1 TTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTCACGCTGAGGT
**
1632 ATTTTCATTTTTTTTTCT-TTTTTCAAAAAATCAACTCATA-T--GAGAGTGAGTTGAGCCTC-G
65 A--TT--TTTTAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGTGAGTTGAGCCTCGG
*
1692 GTCACGCTGAGGTATTTTCTTTAAA
126 GTCACGCTGAGGTA-TTTCTTTTAA
*
1717 TCTCTGTTTTTCAAAAAAATAAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAG
1 T-TCTGTTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTCACGCTGAG
* *
1782 GTATCTTTTTATTTCTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGTGAGTTG-GCCTC-
63 GTAT-TTTTTAATT-TCTGTTTTTC-AAAAAATCAACTCATATTGCGAGAGTGAGTTGAGCCTCG
1845 GGTCACGCTGAGGTATTT-TTTTAA
125 GGTCACGCTGAGGTATTTCTTTTAA
*
1869 TTTCTGTTTTTTCAAAAAATCAACTCATATTGC-AGAGGTGAGTTGAGCCTCGGGTCATGCTGAG
1 -TTCTG-TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTCACGCTGAG
*
1933 GTATTTTTTATTTTCTGTTTTTCAAAAAATCAACT--TATTGCGAGAGTGAGTTG-GCCTCGGGT
63 GTATTTTTTAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGTGAGTTGAGCCTCGGGT
1995 CACGCTGA--TATTTCTTTTTAA
128 CACGCTGAGGTATTTC-TTTTAA
* * *
2016 TTTCTGTTTTT-TAAAATTCAACTCA-AATGCGAGA-GTGAG-TGAGCCCTCGGGTCACGCTGAG
1 -TTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG-CCTC-GGTCACGCTGAG
* * * * * * *
2077 ATA-TTTTTAATATGTCTTTTT---AAAATCAACT-ATA--AC-AGAGGGAGTTG-GCCTC-GGA
63 GTATTTTTTAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGTGAGTTGAGCCTCGGGT
*
2132 CA-GTGTGAGGTA--T-TTTTAA
128 CACG-CTGAGGTATTTCTTTTAA
* ** * * * ** *
2151 GTTATGTTTTT--TTAAATCAACTC-TA-TAC-AGAGGTG-G-TGAGCTTTGG--ACGCATTCGA
1 -TTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTCACGC-TGAGG
*
2207 TATTTCTTTTAATTTCTGTTTTTTC--AAAAT-AACTCATATTGCGAAAGGTGAAGTTGAGCCTC
64 TA-TT-TTTTAATTTCTG-TTTTTCAAAAAATCAACTCATATTGCGAGA-GTG-AGTTGAGCCTC
* * *
2269 GGGTCACAC-CA-TTATTTCTTTTAAA
124 GGGTCACGCTGAGGTATTTCTTTT-AA
* * * ** *
2294 TTAT-TTTTTAAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCT-GGAAAAGC-GA-GT
1 TTCTGTTTTT-CAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTCACGCTGAGGT
*
2355 ATTAATTTAAAATTTCTGTTTTTC-AAAAATCCAACTCATATTGGCGAGAGGTGAGTTGAGGCCT
65 ATT--TTT-TAATTTCTGTTTTTCAAAAAAT-CAACTCATATT-GCGAGA-GTGAGTTGA-GCCT
* *
2419 CGGGTCACGCCGAGGTA-TTC-TTCAA
123 CGGGTCACGCTGAGGTATTTCTTTTAA
*
2444 TTCATGTTTTTCAAAAAATACAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACATG-TC
1 TTC-TGTTTTTCAAAAAAT-CAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTCAC--GCT-
** * * * * *
2508 GAGGTA-TTTTCGATTT-TGTTTTTC-GAAGATCAACTCATAAT-CAAGAGGTGAGTTGAGTCTC
60 GAGGTATTTTTTAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGA-GTGAGTTGAGCCTC
2569 GGGTC
124 GGGTC
2574 GCGACAGCCG
Statistics
Matches: 985, Mismatches: 78, Indels: 193
0.78 0.06 0.15
Matches are distributed among these distances:
128 4 0.00
129 5 0.01
130 2 0.00
131 3 0.00
132 17 0.02
133 14 0.01
134 18 0.02
135 15 0.02
136 2 0.00
137 10 0.01
138 17 0.02
139 10 0.01
140 16 0.02
141 12 0.01
142 8 0.01
143 20 0.02
144 37 0.04
145 37 0.04
146 56 0.06
147 50 0.05
148 79 0.08
149 36 0.04
150 57 0.06
151 108 0.11
152 136 0.14
153 60 0.06
154 60 0.06
155 19 0.02
156 12 0.01
157 21 0.02
158 30 0.03
159 2 0.00
160 12 0.01
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (149 bp):
TTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTCACGCTGAGGTA
TTTTTTAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGTGAGTTGAGCCTCGGGTCAC
GCTGAGGTATTTCTTTTAA
Found at i:2821 original size:29 final size:30
Alignment explanation
Indices: 2765--2875 Score: 113
Period size: 30 Copynumber: 3.7 Consensus size: 30
2755 TTTACAATTT
* *
2765 TTTTGCATTTTGACCCCAAACTTTTCT-AAA
1 TTTTACATTTTGACCCTAAAC-TTTCTAAAA
*
2795 TTTTACATTTTGACCCAAAACTTTCTAAAA
1 TTTTACATTTTGACCCTAAACTTTCTAAAA
* *
2825 TTATA-ATTTTGACCCTTAGACTTTCTCAAAA
1 TTTTACATTTTGACCC-TAAACTTTCT-AAAA
*
2856 -TTT-CACTTTGACCCTAAACT
1 TTTTACATTTTGACCCTAAACT
2876 CTTAAGAATT
Statistics
Matches: 69, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
29 20 0.29
30 45 0.65
31 4 0.06
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (30 bp):
TTTTACATTTTGACCCTAAACTTTCTAAAA
Found at i:3356 original size:14 final size:15
Alignment explanation
Indices: 3328--3356 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3318 CAATCAAATA
3328 AAGAAAAGAGAAGAG
1 AAGAAAAGAGAAGAG
3343 AAGAAAAG-GAAGAG
1 AAGAAAAGAGAAGAG
3357 GGGAAGAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (15 bp):
AAGAAAAGAGAAGAG
Found at i:4389 original size:18 final size:17
Alignment explanation
Indices: 4325--4398 Score: 58
Period size: 17 Copynumber: 3.9 Consensus size: 17
4315 TCTAAAAAAA
*
4325 TCGTGTTTTCAAAAATTC
1 TCGTG-TTTCAAAAAATC
*
4343 TCATGTTTCAAAAAATTC
1 TCGTGTTTCAAAAAA-TC
4361 TGTTTTCGTGTTTTCAAAAAATC
1 -----TCGTG-TTTCAAAAAATC
4384 TCGTGTTTCAAAAAA
1 TCGTGTTTCAAAAAA
4399 AAATAAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
17 19 0.41
18 11 0.24
23 6 0.13
24 10 0.22
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (17 bp):
TCGTGTTTCAAAAAATC
Found at i:4508 original size:17 final size:18
Alignment explanation
Indices: 4474--4584 Score: 95
Period size: 17 Copynumber: 6.3 Consensus size: 18
4464 AAATTTTGTG
4474 TTTCGTGTTTTCAAAAAT
1 TTTCGTGTTTTCAAAAAT
4492 TTTCGTGTTTT-AAAAAT
1 TTTCGTGTTTTCAAAAAT
*
4509 CTTCGT-TTTTCAAAAAT
1 TTTCGTGTTTTCAAAAAT
* * *
4526 TCTGGCG-TTTC-AAAAT
1 TTTCGTGTTTTCAAAAAT
* * *
4542 TTTCTGTTTTTTTTAAAAAA
1 TTTC-G-TGTTTTCAAAAAT
* *
4562 TTACGTGTTTTCACAAAT
1 TTTCGTGTTTTCAAAAAT
4580 TTTCG
1 TTTCG
4585 CATTTCAAAT
Statistics
Matches: 70, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
16 11 0.16
17 24 0.34
18 24 0.34
19 4 0.06
20 7 0.10
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.50
Consensus pattern (18 bp):
TTTCGTGTTTTCAAAAAT
Found at i:4604 original size:54 final size:53
Alignment explanation
Indices: 4499--4604 Score: 117
Period size: 54 Copynumber: 2.0 Consensus size: 53
4489 AATTTTCGTG
* * * *
4499 TTTTAAAAATCTTCGTTTTTCAAAAATTCTGGCGTTTCAAAATTTTCTGTTTT
1 TTTTAAAAATCTACGTTTTTCAAAAATTCTCGCATTTCAAAATTCTCTGTTTT
* *
4552 TTTTAAAAAAT-TACGTGTTTTCACAAATTTTCGCATTTC-AAATTCTCGTGTTT
1 TTTT-AAAAATCTACGT-TTTTCAAAAATTCTCGCATTTCAAAATTCTC-TGTTT
4605 CAAAAACTCC
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
53 15 0.34
54 29 0.66
ACGTcount: A:0.27, C:0.14, G:0.09, T:0.49
Consensus pattern (53 bp):
TTTTAAAAATCTACGTTTTTCAAAAATTCTCGCATTTCAAAATTCTCTGTTTT
Found at i:4716 original size:16 final size:16
Alignment explanation
Indices: 4685--4857 Score: 113
Period size: 17 Copynumber: 10.4 Consensus size: 16
4675 GTTTTTTAAA
* *
4685 TCGTGTTTCAAAAAATG
1 TCGTGTTT-TAAAAATT
4702 TCGTGTTTTAAAAATTT
1 TCGTGTTTTAAAAA-TT
4719 TCGTGTTTCT--AAATT
1 TCGTGTTT-TAAAAATT
*
4734 TCCCTGTTTTAAAAATT
1 T-CGTGTTTTAAAAATT
* * *
4751 CCCGTGTTTCAAAAAAAATG
1 -TCGTGTTT---TAAAAATT
* *
4771 TCTTGTTTTAAAATTT
1 TCGTGTTTTAAAAATT
4787 TCGTGTTTCTAAAAATT
1 TCGTGTTT-TAAAAATT
*
4804 TCGTGTTTT-TAAATT
1 TCGTGTTTTAAAAATT
*
4819 TCGTG-TTT-ACAATT
1 TCGTGTTTTAAAAATT
*
4833 CTCGTGTTTTCAAAATT
1 -TCGTGTTTTAAAAATT
4850 CTCGTGTT
1 -TCGTGTT
4858 AAAAAAAACT
Statistics
Matches: 125, Mismatches: 18, Indels: 26
0.74 0.11 0.15
Matches are distributed among these distances:
14 7 0.06
15 19 0.15
16 30 0.24
17 56 0.45
18 1 0.01
19 6 0.05
20 6 0.05
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (16 bp):
TCGTGTTTTAAAAATT
Found at i:4840 original size:30 final size:31
Alignment explanation
Indices: 4774--4857 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 31
4764 AAAAATGTCT
* *
4774 TGTTTT-AAAATTTTCGTGTTTCTAAAAATTTCG
1 TGTTTTCAAAATTCTCGTG-TT-T-ACAATTTCG
*
4807 TGTTTT-TAAATT-TCGTGTTTACAATTCTCG
1 TGTTTTCAAAATTCTCGTGTTTACAATT-TCG
4837 TGTTTTCAAAATTCTCGTGTT
1 TGTTTTCAAAATTCTCGTGTT
4858 AAAAAAAACT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
29 5 0.11
30 10 0.22
31 7 0.16
32 12 0.27
33 11 0.24
ACGTcount: A:0.23, C:0.12, G:0.13, T:0.52
Consensus pattern (31 bp):
TGTTTTCAAAATTCTCGTGTTTACAATTTCG
Found at i:9484 original size:21 final size:22
Alignment explanation
Indices: 9456--9505 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
9446 TTTTGAAACC
9456 CAAG-TTCAAGA-TTTATGATT
1 CAAGATTCAAGAGTTTATGATT
* *
9476 CGAGATTC-AGAGTTTGTGATT
1 CAAGATTCAAGAGTTTATGATT
9497 CAAGATTCA
1 CAAGATTCA
9506 GGGTTTAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (22 bp):
CAAGATTCAAGAGTTTATGATT
Found at i:9517 original size:21 final size:21
Alignment explanation
Indices: 9467--9517 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
9457 AAGTTCAAGA
*
9467 TTTATGATTCGAGATTCAGAG
1 TTTATGATTCAAGATTCAGAG
* *
9488 TTTGTGATTCAAGATTCAGGG
1 TTTATGATTCAAGATTCAGAG
*
9509 TTTAAGATT
1 TTTATGATT
9518 TGAAGTTTGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.08, G:0.24, T:0.41
Consensus pattern (21 bp):
TTTATGATTCAAGATTCAGAG
Found at i:14066 original size:22 final size:21
Alignment explanation
Indices: 14035--14085 Score: 84
Period size: 22 Copynumber: 2.4 Consensus size: 21
14025 ATAGTCTGAC
14035 AAAAAAAAATTAAAAAAGTGA
1 AAAAAAAAATTAAAAAAGTGA
*
14056 AAAGAAAAAATTGAAAAAGTGA
1 AAA-AAAAAATTAAAAAAGTGA
14078 AAAAAAAA
1 AAAAAAAA
14086 TTACTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (21 bp):
AAAAAAAAATTAAAAAAGTGA
Found at i:26034 original size:27 final size:28
Alignment explanation
Indices: 25958--26042 Score: 93
Period size: 27 Copynumber: 3.0 Consensus size: 28
25948 TTTGGCCCAA
* *
25958 TTTGGTATCTAAACTTGACACTTTTTCCTAA
1 TTTGGTACCTAAACTTGACAC-TTTT-CT-T
*
25989 TTT-ATACCTAAACTTGACACTTTTCTT
1 TTTGGTACCTAAACTTGACACTTTTCTT
*
26016 TTTGGTA-CTAAACTTGACATTTTTCTT
1 TTTGGTACCTAAACTTGACACTTTTCTT
26043 AAGTTGGTAC
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
27 22 0.46
28 4 0.08
29 4 0.08
30 15 0.31
31 3 0.06
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.48
Consensus pattern (28 bp):
TTTGGTACCTAAACTTGACACTTTTCTT
Found at i:26123 original size:59 final size:57
Alignment explanation
Indices: 25898--26123 Score: 176
Period size: 59 Copynumber: 3.9 Consensus size: 57
25888 CTTAATATAC
* * * * * * *
25898 ATTTAGTACCTAAATTTGACACTTTTTCATAATTTGGTACCTAAACTTTGTTTGGCCCA
1 ATTTGGTATCTAAACTTGACA-TTTTTCCTAATTTGATACCTAAACTTT-TTTGGTCTA
*
25957 ATTTGGTATCTAAACTTGACACTTTTTCCTAATTT-ATACCTAAACTTGACACTTT--TCT-
1 ATTTGGTATCTAAACTTGACA-TTTTTCCTAATTTGATACCTAAACTT----TTTTGGTCTA
* * * * * * *
26015 TTTTGGTA-CTAAACTTGACATTTTTCTTAAGTTGGTACTTAATCCTTTTTGGGATCTA
1 ATTTGGTATCTAAACTTGACATTTTTCCTAATTTGATACCTAA-ACTTTTTTGG-TCTA
*
26073 ATTTGGTATCTAAACTTGACTTTTTTTCCTAATTTGATACCT-AACTTTTTT
1 ATTTGGTATCTAAACTTGAC-ATTTTTCCTAATTTGATACCTAAACTTTTTT
26124 TTTTGATTTG
Statistics
Matches: 131, Mismatches: 24, Indels: 25
0.73 0.13 0.14
Matches are distributed among these distances:
54 2 0.02
56 11 0.08
57 21 0.16
58 34 0.26
59 44 0.34
60 16 0.12
61 3 0.02
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.47
Consensus pattern (57 bp):
ATTTGGTATCTAAACTTGACATTTTTCCTAATTTGATACCTAAACTTTTTTGGTCTA
Done.